## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF4 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1    ORF7 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1    ORF9 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1   ORF20 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1   ORF21 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1   ORF31 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       1   ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13:       1   ORF34 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 14:       1   ORF38 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 15:       1   ORF50 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 16:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 17:       1   ORF56 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 18:       1   ORF61 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 19:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 20:       1  NOIR_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 21:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 22:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 23:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 24:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 25:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 31:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 32:       2   ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 33:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 34:       2   ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 35:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 36:       2   ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 37:       2   ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 38:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 39:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 40:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 41:       2   ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 42:       3    ORF6 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 43:       3   ORF70 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 44:       4    ORF8 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 45:       4   ORF12 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 46:       4   ORF13 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 47:       4   ORF15 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 48:       4   ORF16 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 49:       4   ORF22 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 50:       4   ORF23 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 51:       4   ORF24 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 52:       4   ORF25 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 53:       4   ORF27 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 54:       4   ORF33 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 55:       4 ORF35.5 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 56:       4   ORF35 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 57:       4   ORF36 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 58:       4   ORF39 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 59:       4     CTO 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 60:       4   ORF40 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 61:       4   ORF41 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 62:       4   ORF42 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 63:       4   ORF43 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 64:       4   ORF44 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 65:       4   ORF45 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 66:       4   ORF46 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 67:       4   ORF48 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 68:       4   ORF52 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 69:       4   ORF54 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 70:       4   ORF57 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 71:       4   ORF58 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 72:       4   ORF59 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 73:       4   ORF60 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 74:       4   ORF62 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 75:       4   ORF68 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 76:       4   ORF71 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 77:       4   ORF72 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 78:       5 ORF64_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 79:       5   ORF75 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.004412661 -1.9247386 1.0297672 0.6455362
## 14: 0.004412661 -1.9247386 1.0297672 0.6455362
## 15: 0.004412661 -1.9247386 1.0297672 0.6455362
## 16: 0.004412661 -1.9247386 1.0297672 0.6455362
## 17: 0.004412661 -1.9247386 1.0297672 0.6455362
## 18: 0.004412661 -1.9247386 1.0297672 0.6455362
## 19: 0.004412661 -1.9247386 1.0297672 0.6455362
## 20: 0.004412661 -1.9247386 1.0297672 0.6455362
## 21: 0.004412661 -1.9247386 1.0297672 0.6455362
## 22: 0.004412661 -1.9247386 1.0297672 0.6455362
## 23: 0.004412661 -1.9247386 1.0297672 0.6455362
## 24: 0.004412661 -1.9247386 1.0297672 0.6455362
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.005151525 -0.8707344 0.5400240 0.2113619
## 31: 0.005151525 -0.8707344 0.5400240 0.2113619
## 32: 0.005151525 -0.8707344 0.5400240 0.2113619
## 33: 0.005151525 -0.8707344 0.5400240 0.2113619
## 34: 0.005151525 -0.8707344 0.5400240 0.2113619
## 35: 0.005151525 -0.8707344 0.5400240 0.2113619
## 36: 0.005151525 -0.8707344 0.5400240 0.2113619
## 37: 0.005151525 -0.8707344 0.5400240 0.2113619
## 38: 0.005151525 -0.8707344 0.5400240 0.2113619
## 39: 0.005151525 -0.8707344 0.5400240 0.2113619
## 40: 0.005151525 -0.8707344 0.5400240 0.2113619
## 41: 0.005151525 -0.8707344 0.5400240 0.2113619
## 42: 0.004425869 -1.9892346 1.0926661 0.5323203
## 43: 0.004425869 -1.9892346 1.0926661 0.5323203
## 44: 0.005261677 -1.1191772 0.8688403 0.4684034
## 45: 0.005261677 -1.1191772 0.8688403 0.4684034
## 46: 0.005261677 -1.1191772 0.8688403 0.4684034
## 47: 0.005261677 -1.1191772 0.8688403 0.4684034
## 48: 0.005261677 -1.1191772 0.8688403 0.4684034
## 49: 0.005261677 -1.1191772 0.8688403 0.4684034
## 50: 0.005261677 -1.1191772 0.8688403 0.4684034
## 51: 0.005261677 -1.1191772 0.8688403 0.4684034
## 52: 0.005261677 -1.1191772 0.8688403 0.4684034
## 53: 0.005261677 -1.1191772 0.8688403 0.4684034
## 54: 0.005261677 -1.1191772 0.8688403 0.4684034
## 55: 0.005261677 -1.1191772 0.8688403 0.4684034
## 56: 0.005261677 -1.1191772 0.8688403 0.4684034
## 57: 0.005261677 -1.1191772 0.8688403 0.4684034
## 58: 0.005261677 -1.1191772 0.8688403 0.4684034
## 59: 0.005261677 -1.1191772 0.8688403 0.4684034
## 60: 0.005261677 -1.1191772 0.8688403 0.4684034
## 61: 0.005261677 -1.1191772 0.8688403 0.4684034
## 62: 0.005261677 -1.1191772 0.8688403 0.4684034
## 63: 0.005261677 -1.1191772 0.8688403 0.4684034
## 64: 0.005261677 -1.1191772 0.8688403 0.4684034
## 65: 0.005261677 -1.1191772 0.8688403 0.4684034
## 66: 0.005261677 -1.1191772 0.8688403 0.4684034
## 67: 0.005261677 -1.1191772 0.8688403 0.4684034
## 68: 0.005261677 -1.1191772 0.8688403 0.4684034
## 69: 0.005261677 -1.1191772 0.8688403 0.4684034
## 70: 0.005261677 -1.1191772 0.8688403 0.4684034
## 71: 0.005261677 -1.1191772 0.8688403 0.4684034
## 72: 0.005261677 -1.1191772 0.8688403 0.4684034
## 73: 0.005261677 -1.1191772 0.8688403 0.4684034
## 74: 0.005261677 -1.1191772 0.8688403 0.4684034
## 75: 0.005261677 -1.1191772 0.8688403 0.4684034
## 76: 0.005261677 -1.1191772 0.8688403 0.4684034
## 77: 0.005261677 -1.1191772 0.8688403 0.4684034
## 78: 0.005245917 -0.8139770 1.0031408 0.7004716
## 79: 0.005245917 -0.8139770 1.0031408 0.7004716
##           se.bp          v         c      pchi

## [1] "ORF32"   "ORF9"    "ORF67_1" "ORF40"   "ORF59"   "ORF36"   "ORF39"  
## [8] "ORF8"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"
## [1] 17

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF4 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1    ORF7 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1    ORF9 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1   ORF20 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1   ORF21 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1   ORF31 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       1   ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13:       1   ORF34 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 14:       1   ORF38 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 15:       1   ORF50 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 16:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 17:       1   ORF56 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 18:       1   ORF61 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 19:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 20:       1  NOIR_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 21:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 22:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 23:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 24:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 25:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 31:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 32:       2   ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 33:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 34:       2   ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 35:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 36:       2   ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 37:       2   ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 38:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 39:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 40:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 41:       2   ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 42:       3    ORF6 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 43:       3   ORF70 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 44:       4    ORF8 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 45:       4   ORF12 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 46:       4   ORF13 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 47:       4   ORF15 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 48:       4   ORF16 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 49:       4   ORF22 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 50:       4   ORF23 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 51:       4   ORF24 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 52:       4   ORF25 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 53:       4   ORF27 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 54:       4   ORF33 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 55:       4 ORF35.5 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 56:       4   ORF35 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 57:       4   ORF36 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 58:       4   ORF39 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 59:       4     CTO 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 60:       4   ORF40 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 61:       4   ORF41 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 62:       4   ORF42 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 63:       4   ORF43 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 64:       4   ORF44 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 65:       4   ORF46 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 66:       4   ORF48 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 67:       4   ORF52 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 68:       4   ORF54 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 69:       4   ORF57 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 70:       4   ORF58 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 71:       4   ORF59 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 72:       4   ORF60 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 73:       4   ORF62 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 74:       4   ORF68 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 75:       4   ORF71 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 76:       4   ORF72 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 77:       5   ORF45 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 78:       6 ORF64_1 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 79:       6   ORF75 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.004412661 -1.9247386 1.0297672 0.6455362
## 14: 0.004412661 -1.9247386 1.0297672 0.6455362
## 15: 0.004412661 -1.9247386 1.0297672 0.6455362
## 16: 0.004412661 -1.9247386 1.0297672 0.6455362
## 17: 0.004412661 -1.9247386 1.0297672 0.6455362
## 18: 0.004412661 -1.9247386 1.0297672 0.6455362
## 19: 0.004412661 -1.9247386 1.0297672 0.6455362
## 20: 0.004412661 -1.9247386 1.0297672 0.6455362
## 21: 0.004412661 -1.9247386 1.0297672 0.6455362
## 22: 0.004412661 -1.9247386 1.0297672 0.6455362
## 23: 0.004412661 -1.9247386 1.0297672 0.6455362
## 24: 0.004412661 -1.9247386 1.0297672 0.6455362
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.005151525 -0.8707344 0.5400240 0.2113619
## 31: 0.005151525 -0.8707344 0.5400240 0.2113619
## 32: 0.005151525 -0.8707344 0.5400240 0.2113619
## 33: 0.005151525 -0.8707344 0.5400240 0.2113619
## 34: 0.005151525 -0.8707344 0.5400240 0.2113619
## 35: 0.005151525 -0.8707344 0.5400240 0.2113619
## 36: 0.005151525 -0.8707344 0.5400240 0.2113619
## 37: 0.005151525 -0.8707344 0.5400240 0.2113619
## 38: 0.005151525 -0.8707344 0.5400240 0.2113619
## 39: 0.005151525 -0.8707344 0.5400240 0.2113619
## 40: 0.005151525 -0.8707344 0.5400240 0.2113619
## 41: 0.005151525 -0.8707344 0.5400240 0.2113619
## 42: 0.004425869 -1.9892346 1.0926661 0.5323203
## 43: 0.004425869 -1.9892346 1.0926661 0.5323203
## 44: 0.005261677 -1.1191772 0.8688403 0.4684034
## 45: 0.005261677 -1.1191772 0.8688403 0.4684034
## 46: 0.005261677 -1.1191772 0.8688403 0.4684034
## 47: 0.005261677 -1.1191772 0.8688403 0.4684034
## 48: 0.005261677 -1.1191772 0.8688403 0.4684034
## 49: 0.005261677 -1.1191772 0.8688403 0.4684034
## 50: 0.005261677 -1.1191772 0.8688403 0.4684034
## 51: 0.005261677 -1.1191772 0.8688403 0.4684034
## 52: 0.005261677 -1.1191772 0.8688403 0.4684034
## 53: 0.005261677 -1.1191772 0.8688403 0.4684034
## 54: 0.005261677 -1.1191772 0.8688403 0.4684034
## 55: 0.005261677 -1.1191772 0.8688403 0.4684034
## 56: 0.005261677 -1.1191772 0.8688403 0.4684034
## 57: 0.005261677 -1.1191772 0.8688403 0.4684034
## 58: 0.005261677 -1.1191772 0.8688403 0.4684034
## 59: 0.005261677 -1.1191772 0.8688403 0.4684034
## 60: 0.005261677 -1.1191772 0.8688403 0.4684034
## 61: 0.005261677 -1.1191772 0.8688403 0.4684034
## 62: 0.005261677 -1.1191772 0.8688403 0.4684034
## 63: 0.005261677 -1.1191772 0.8688403 0.4684034
## 64: 0.005261677 -1.1191772 0.8688403 0.4684034
## 65: 0.005261677 -1.1191772 0.8688403 0.4684034
## 66: 0.005261677 -1.1191772 0.8688403 0.4684034
## 67: 0.005261677 -1.1191772 0.8688403 0.4684034
## 68: 0.005261677 -1.1191772 0.8688403 0.4684034
## 69: 0.005261677 -1.1191772 0.8688403 0.4684034
## 70: 0.005261677 -1.1191772 0.8688403 0.4684034
## 71: 0.005261677 -1.1191772 0.8688403 0.4684034
## 72: 0.005261677 -1.1191772 0.8688403 0.4684034
## 73: 0.005261677 -1.1191772 0.8688403 0.4684034
## 74: 0.005261677 -1.1191772 0.8688403 0.4684034
## 75: 0.005261677 -1.1191772 0.8688403 0.4684034
## 76: 0.005261677 -1.1191772 0.8688403 0.4684034
## 77: 0.005245917 -0.8139770 1.0031408 0.7004716
## 78: 0.004284669 -0.4169704 1.2196713 0.9030615
## 79: 0.004284669 -0.4169704 1.2196713 0.9030615
##           se.bp          v         c      pchi

## [1] "ORF32"   "ORF9"    "ORF67_1" "ORF59"   "ORF36"   "ORF8"    "ORF39"
## [1] 7
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"   "ORF64_1" "ORF75"
## [1] 19

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20:       2   ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22:       2   ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24:       2   ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 25:       2   ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29:       2   ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30:       3    ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31:       3    ORF7 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32:       3    ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33:       3   ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 34:       3   ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 35:       3   ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 36:       3   ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 37:       3   ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 38:       3   ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 39:       3   ORF56 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 40:       3   ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 41:       3  NOIR_1 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 42:       4    ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 43:       4   ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 44:       5    ORF8 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 45:       5   ORF12 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 46:       5   ORF13 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 47:       5   ORF15 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 48:       5   ORF16 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 49:       5   ORF22 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 50:       5   ORF23 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 51:       5   ORF24 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 52:       5   ORF25 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 53:       5   ORF27 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 54:       5   ORF33 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 55:       5 ORF35.5 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 56:       5   ORF35 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 57:       5   ORF36 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 58:       5   ORF39 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 59:       5     CTO 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 60:       5   ORF40 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 61:       5   ORF41 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 62:       5   ORF42 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 63:       5   ORF43 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 64:       5   ORF44 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 65:       5   ORF46 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 66:       5   ORF48 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 67:       5   ORF52 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 68:       5   ORF54 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 69:       5   ORF57 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 70:       5   ORF58 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 71:       5   ORF59 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 72:       5   ORF60 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 73:       5   ORF62 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 74:       5   ORF68 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 75:       5   ORF71 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 76:       5   ORF72 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 77:       6   ORF45 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 78:       7 ORF64_1 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 79:       7   ORF75 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.005151525 -0.8707344 0.5400240 0.2113619
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.004425869 -1.9892346 1.0926661 0.5323203
## 34: 0.004425869 -1.9892346 1.0926661 0.5323203
## 35: 0.004425869 -1.9892346 1.0926661 0.5323203
## 36: 0.004425869 -1.9892346 1.0926661 0.5323203
## 37: 0.004425869 -1.9892346 1.0926661 0.5323203
## 38: 0.004425869 -1.9892346 1.0926661 0.5323203
## 39: 0.004425869 -1.9892346 1.0926661 0.5323203
## 40: 0.004425869 -1.9892346 1.0926661 0.5323203
## 41: 0.004425869 -1.9892346 1.0926661 0.5323203
## 42: 0.005261677 -1.1191772 0.8688403 0.4684034
## 43: 0.005261677 -1.1191772 0.8688403 0.4684034
## 44: 0.005245917 -0.8139770 1.0031408 0.7004716
## 45: 0.005245917 -0.8139770 1.0031408 0.7004716
## 46: 0.005245917 -0.8139770 1.0031408 0.7004716
## 47: 0.005245917 -0.8139770 1.0031408 0.7004716
## 48: 0.005245917 -0.8139770 1.0031408 0.7004716
## 49: 0.005245917 -0.8139770 1.0031408 0.7004716
## 50: 0.005245917 -0.8139770 1.0031408 0.7004716
## 51: 0.005245917 -0.8139770 1.0031408 0.7004716
## 52: 0.005245917 -0.8139770 1.0031408 0.7004716
## 53: 0.005245917 -0.8139770 1.0031408 0.7004716
## 54: 0.005245917 -0.8139770 1.0031408 0.7004716
## 55: 0.005245917 -0.8139770 1.0031408 0.7004716
## 56: 0.005245917 -0.8139770 1.0031408 0.7004716
## 57: 0.005245917 -0.8139770 1.0031408 0.7004716
## 58: 0.005245917 -0.8139770 1.0031408 0.7004716
## 59: 0.005245917 -0.8139770 1.0031408 0.7004716
## 60: 0.005245917 -0.8139770 1.0031408 0.7004716
## 61: 0.005245917 -0.8139770 1.0031408 0.7004716
## 62: 0.005245917 -0.8139770 1.0031408 0.7004716
## 63: 0.005245917 -0.8139770 1.0031408 0.7004716
## 64: 0.005245917 -0.8139770 1.0031408 0.7004716
## 65: 0.005245917 -0.8139770 1.0031408 0.7004716
## 66: 0.005245917 -0.8139770 1.0031408 0.7004716
## 67: 0.005245917 -0.8139770 1.0031408 0.7004716
## 68: 0.005245917 -0.8139770 1.0031408 0.7004716
## 69: 0.005245917 -0.8139770 1.0031408 0.7004716
## 70: 0.005245917 -0.8139770 1.0031408 0.7004716
## 71: 0.005245917 -0.8139770 1.0031408 0.7004716
## 72: 0.005245917 -0.8139770 1.0031408 0.7004716
## 73: 0.005245917 -0.8139770 1.0031408 0.7004716
## 74: 0.005245917 -0.8139770 1.0031408 0.7004716
## 75: 0.005245917 -0.8139770 1.0031408 0.7004716
## 76: 0.005245917 -0.8139770 1.0031408 0.7004716
## 77: 0.004284669 -0.4169704 1.2196713 0.9030615
## 78: 0.005111506 -0.7566956 1.0826127 0.7640431
## 79: 0.005111506 -0.7566956 1.0826127 0.7640431
##           se.bp          v         c      pchi

## [1] "ORF32" "ORF59" "ORF36" "ORF8"  "ORF39"
## [1] 5
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"   "ORF45"
## [1] 18

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20:       2   ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22:       2   ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23:       2   ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 25:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27:       2   ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28:       3    ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29:       3    ORF7 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30:       3    ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31:       3   ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32:       3   ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33:       3   ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 34:       3   ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 35:       3   ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 36:       3   ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 37:       3   ORF56 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 38:       3   ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 39:       3  NOIR_1 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 40:       4    ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 41:       4   ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 42:       5    ORF8 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 43:       5   ORF22 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 44:       5   ORF23 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 45:       5   ORF24 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 46:       5   ORF25 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 47:       5   ORF27 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 48:       5   ORF33 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 49:       5 ORF35.5 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 50:       5   ORF36 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 51:       5   ORF39 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 52:       5     CTO 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 53:       5   ORF40 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 54:       5   ORF42 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 55:       5   ORF43 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 56:       5   ORF44 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 57:       5   ORF46 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 58:       5   ORF48 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 59:       5   ORF58 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 60:       5   ORF59 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 61:       5   ORF62 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 62:       5   ORF68 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 63:       6   ORF12 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 64:       6   ORF13 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 65:       6   ORF15 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 66:       6   ORF16 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 67:       6   ORF35 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 68:       6   ORF41 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 69:       6   ORF52 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 70:       6   ORF54 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 71:       6   ORF57 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 72:       6   ORF60 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 73:       6   ORF71 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 74:       6   ORF72 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 75:       7   ORF28 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 76:       8   ORF32 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 77:       9   ORF45 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 78:      10 ORF64_1 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 79:      10   ORF75 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.005151525 -0.8707344 0.5400240 0.2113619
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.004425869 -1.9892346 1.0926661 0.5323203
## 34: 0.004425869 -1.9892346 1.0926661 0.5323203
## 35: 0.004425869 -1.9892346 1.0926661 0.5323203
## 36: 0.004425869 -1.9892346 1.0926661 0.5323203
## 37: 0.004425869 -1.9892346 1.0926661 0.5323203
## 38: 0.004425869 -1.9892346 1.0926661 0.5323203
## 39: 0.004425869 -1.9892346 1.0926661 0.5323203
## 40: 0.005261677 -1.1191772 0.8688403 0.4684034
## 41: 0.005261677 -1.1191772 0.8688403 0.4684034
## 42: 0.005245917 -0.8139770 1.0031408 0.7004716
## 43: 0.005245917 -0.8139770 1.0031408 0.7004716
## 44: 0.005245917 -0.8139770 1.0031408 0.7004716
## 45: 0.005245917 -0.8139770 1.0031408 0.7004716
## 46: 0.005245917 -0.8139770 1.0031408 0.7004716
## 47: 0.005245917 -0.8139770 1.0031408 0.7004716
## 48: 0.005245917 -0.8139770 1.0031408 0.7004716
## 49: 0.005245917 -0.8139770 1.0031408 0.7004716
## 50: 0.005245917 -0.8139770 1.0031408 0.7004716
## 51: 0.005245917 -0.8139770 1.0031408 0.7004716
## 52: 0.005245917 -0.8139770 1.0031408 0.7004716
## 53: 0.005245917 -0.8139770 1.0031408 0.7004716
## 54: 0.005245917 -0.8139770 1.0031408 0.7004716
## 55: 0.005245917 -0.8139770 1.0031408 0.7004716
## 56: 0.005245917 -0.8139770 1.0031408 0.7004716
## 57: 0.005245917 -0.8139770 1.0031408 0.7004716
## 58: 0.005245917 -0.8139770 1.0031408 0.7004716
## 59: 0.005245917 -0.8139770 1.0031408 0.7004716
## 60: 0.005245917 -0.8139770 1.0031408 0.7004716
## 61: 0.005245917 -0.8139770 1.0031408 0.7004716
## 62: 0.005245917 -0.8139770 1.0031408 0.7004716
## 63: 0.004284669 -0.4169704 1.2196713 0.9030615
## 64: 0.004284669 -0.4169704 1.2196713 0.9030615
## 65: 0.004284669 -0.4169704 1.2196713 0.9030615
## 66: 0.004284669 -0.4169704 1.2196713 0.9030615
## 67: 0.004284669 -0.4169704 1.2196713 0.9030615
## 68: 0.004284669 -0.4169704 1.2196713 0.9030615
## 69: 0.004284669 -0.4169704 1.2196713 0.9030615
## 70: 0.004284669 -0.4169704 1.2196713 0.9030615
## 71: 0.004284669 -0.4169704 1.2196713 0.9030615
## 72: 0.004284669 -0.4169704 1.2196713 0.9030615
## 73: 0.004284669 -0.4169704 1.2196713 0.9030615
## 74: 0.004284669 -0.4169704 1.2196713 0.9030615
## 75: 0.005111506 -0.7566956 1.0826127 0.7640431
## 76: 0.005030398 -0.6409917 1.0274941 0.1121456
## 77: 0.005288863 -0.9230106 1.0459982 0.4260979
## 78: 0.004655777 -0.6065374 1.2287410 0.6115571
## 79: 0.004655777 -0.6065374 1.2287410 0.6115571
##           se.bp          v         c      pchi

## [1] "ORF49" "ORF74" "ORF55" "ORF73" "ORF62" "ORF48"
## [1] 6
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1" "ORF73"  
## [15] "ORF74"   "ORF76"   "ORF12"   "ORF13"   "ORF15"   "ORF16"   "ORF35"  
## [22] "ORF41"   "ORF52"   "ORF54"   "ORF57"   "ORF60"   "ORF71"   "ORF72"
## [1] 28

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24:       3    ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 25:       3    ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 26:       3   ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 27:       3   ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 28:       3   ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29:       3   ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30:       3   ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31:       3   ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32:       3   ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33:       4    ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 34:       4   ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 35:       5    ORF7 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 36:       5   ORF56 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 37:       5  NOIR_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 38:       6    ORF8 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 39:       6   ORF22 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 40:       6   ORF23 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 41:       6   ORF24 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 42:       6   ORF25 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 43:       6   ORF27 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 44:       6   ORF33 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 45:       6 ORF35.5 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 46:       6   ORF36 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 47:       6   ORF39 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 48:       6     CTO 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 49:       6   ORF40 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 50:       6   ORF42 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 51:       6   ORF43 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 52:       6   ORF44 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 53:       6   ORF46 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 54:       6   ORF48 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 55:       6   ORF58 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 56:       6   ORF59 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 57:       6   ORF62 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 58:       6   ORF68 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 59:       7   ORF12 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 60:       7   ORF13 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 61:       7   ORF15 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 62:       7   ORF16 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 63:       7   ORF35 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 64:       7   ORF41 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 65:       7   ORF52 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 66:       7   ORF54 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 67:       7   ORF57 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 68:       7   ORF60 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 69:       7   ORF71 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 70:       7   ORF72 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 71:       8   ORF28 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 72:       9   ORF32 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 73:      10   ORF37 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 74:      10   ORF51 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 75:      10   ORF55 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 76:      10   ORF76 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 77:      11   ORF45 0.8717656 0.9745309 0.6021179 0.016716342 0.0046060056
## 78:      12 ORF64_1 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## 79:      12   ORF75 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.004425869 -1.9892346 1.0926661 0.5323203
## 25: 0.004425869 -1.9892346 1.0926661 0.5323203
## 26: 0.004425869 -1.9892346 1.0926661 0.5323203
## 27: 0.004425869 -1.9892346 1.0926661 0.5323203
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.005261677 -1.1191772 0.8688403 0.4684034
## 34: 0.005261677 -1.1191772 0.8688403 0.4684034
## 35: 0.005245917 -0.8139770 1.0031408 0.7004716
## 36: 0.005245917 -0.8139770 1.0031408 0.7004716
## 37: 0.005245917 -0.8139770 1.0031408 0.7004716
## 38: 0.004284669 -0.4169704 1.2196713 0.9030615
## 39: 0.004284669 -0.4169704 1.2196713 0.9030615
## 40: 0.004284669 -0.4169704 1.2196713 0.9030615
## 41: 0.004284669 -0.4169704 1.2196713 0.9030615
## 42: 0.004284669 -0.4169704 1.2196713 0.9030615
## 43: 0.004284669 -0.4169704 1.2196713 0.9030615
## 44: 0.004284669 -0.4169704 1.2196713 0.9030615
## 45: 0.004284669 -0.4169704 1.2196713 0.9030615
## 46: 0.004284669 -0.4169704 1.2196713 0.9030615
## 47: 0.004284669 -0.4169704 1.2196713 0.9030615
## 48: 0.004284669 -0.4169704 1.2196713 0.9030615
## 49: 0.004284669 -0.4169704 1.2196713 0.9030615
## 50: 0.004284669 -0.4169704 1.2196713 0.9030615
## 51: 0.004284669 -0.4169704 1.2196713 0.9030615
## 52: 0.004284669 -0.4169704 1.2196713 0.9030615
## 53: 0.004284669 -0.4169704 1.2196713 0.9030615
## 54: 0.004284669 -0.4169704 1.2196713 0.9030615
## 55: 0.004284669 -0.4169704 1.2196713 0.9030615
## 56: 0.004284669 -0.4169704 1.2196713 0.9030615
## 57: 0.004284669 -0.4169704 1.2196713 0.9030615
## 58: 0.004284669 -0.4169704 1.2196713 0.9030615
## 59: 0.005111506 -0.7566956 1.0826127 0.7640431
## 60: 0.005111506 -0.7566956 1.0826127 0.7640431
## 61: 0.005111506 -0.7566956 1.0826127 0.7640431
## 62: 0.005111506 -0.7566956 1.0826127 0.7640431
## 63: 0.005111506 -0.7566956 1.0826127 0.7640431
## 64: 0.005111506 -0.7566956 1.0826127 0.7640431
## 65: 0.005111506 -0.7566956 1.0826127 0.7640431
## 66: 0.005111506 -0.7566956 1.0826127 0.7640431
## 67: 0.005111506 -0.7566956 1.0826127 0.7640431
## 68: 0.005111506 -0.7566956 1.0826127 0.7640431
## 69: 0.005111506 -0.7566956 1.0826127 0.7640431
## 70: 0.005111506 -0.7566956 1.0826127 0.7640431
## 71: 0.005030398 -0.6409917 1.0274941 0.1121456
## 72: 0.005288863 -0.9230106 1.0459982 0.4260979
## 73: 0.004655777 -0.6065374 1.2287410 0.6115571
## 74: 0.004655777 -0.6065374 1.2287410 0.6115571
## 75: 0.004655777 -0.6065374 1.2287410 0.6115571
## 76: 0.004655777 -0.6065374 1.2287410 0.6115571
## 77: 0.005269934 -1.1054164 0.8465835 0.5423247
## 78: 0.004283939 -0.4807691 1.2864858 0.2612100
## 79: 0.004283939 -0.4807691 1.2864858 0.2612100
##           se.bp          v         c      pchi

## [1] "NOIR_2" "ORF1"   "ORF36"  "ORF59"  "ORF8"   "ORF39"  "ORF62"  "ORF48"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  2:       1    ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  3:       1   ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  4:       1   ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  5:       1   ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  6:       1   ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  7:       1   ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  8:       1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
##  9:       1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10:       1   ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11:       1  NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12:       2    ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13:       2    ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14:       2   ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15:       2   ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16:       2   ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17:       2   ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18:       2   ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19:       2   ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20:       2   ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21:       2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22:       2   ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23:       2   ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24:       3    ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 25:       3    ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 26:       3   ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 27:       3   ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 28:       3   ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29:       3   ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30:       3   ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31:       3   ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32:       3   ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33:       4    ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 34:       4   ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 35:       5    ORF7 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 36:       5   ORF56 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 37:       5  NOIR_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 38:       6    ORF8 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 39:       6   ORF22 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 40:       6   ORF23 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 41:       6   ORF24 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 42:       6   ORF25 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 43:       6   ORF27 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 44:       6   ORF33 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 45:       6 ORF35.5 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 46:       6   ORF36 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 47:       6   ORF39 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 48:       6     CTO 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 49:       6   ORF40 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 50:       6   ORF42 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 51:       6   ORF43 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 52:       6   ORF44 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 53:       6   ORF46 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 54:       6   ORF48 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 55:       6   ORF58 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 56:       6   ORF59 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 57:       6   ORF62 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 58:       6   ORF68 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 59:       7   ORF12 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 60:       7   ORF13 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 61:       7   ORF15 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 62:       7   ORF16 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 63:       7   ORF35 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 64:       7   ORF41 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 65:       7   ORF52 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 66:       7   ORF54 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 67:       7   ORF57 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 68:       7   ORF60 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 69:       7   ORF71 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 70:       7   ORF72 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 71:       8   ORF28 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 72:       9   ORF32 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 73:      10   ORF37 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 74:      10   ORF51 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 75:      10   ORF55 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 76:      10   ORF76 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 77:      11   ORF45 0.8717656 0.9745309 0.6021179 0.016716342 0.0046060056
## 78:      12 ORF64_1 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## 79:      12   ORF75 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004412661 -1.9247386 1.0297672 0.6455362
##  2: 0.004412661 -1.9247386 1.0297672 0.6455362
##  3: 0.004412661 -1.9247386 1.0297672 0.6455362
##  4: 0.004412661 -1.9247386 1.0297672 0.6455362
##  5: 0.004412661 -1.9247386 1.0297672 0.6455362
##  6: 0.004412661 -1.9247386 1.0297672 0.6455362
##  7: 0.004412661 -1.9247386 1.0297672 0.6455362
##  8: 0.004412661 -1.9247386 1.0297672 0.6455362
##  9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.004425869 -1.9892346 1.0926661 0.5323203
## 25: 0.004425869 -1.9892346 1.0926661 0.5323203
## 26: 0.004425869 -1.9892346 1.0926661 0.5323203
## 27: 0.004425869 -1.9892346 1.0926661 0.5323203
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.005261677 -1.1191772 0.8688403 0.4684034
## 34: 0.005261677 -1.1191772 0.8688403 0.4684034
## 35: 0.005245917 -0.8139770 1.0031408 0.7004716
## 36: 0.005245917 -0.8139770 1.0031408 0.7004716
## 37: 0.005245917 -0.8139770 1.0031408 0.7004716
## 38: 0.004284669 -0.4169704 1.2196713 0.9030615
## 39: 0.004284669 -0.4169704 1.2196713 0.9030615
## 40: 0.004284669 -0.4169704 1.2196713 0.9030615
## 41: 0.004284669 -0.4169704 1.2196713 0.9030615
## 42: 0.004284669 -0.4169704 1.2196713 0.9030615
## 43: 0.004284669 -0.4169704 1.2196713 0.9030615
## 44: 0.004284669 -0.4169704 1.2196713 0.9030615
## 45: 0.004284669 -0.4169704 1.2196713 0.9030615
## 46: 0.004284669 -0.4169704 1.2196713 0.9030615
## 47: 0.004284669 -0.4169704 1.2196713 0.9030615
## 48: 0.004284669 -0.4169704 1.2196713 0.9030615
## 49: 0.004284669 -0.4169704 1.2196713 0.9030615
## 50: 0.004284669 -0.4169704 1.2196713 0.9030615
## 51: 0.004284669 -0.4169704 1.2196713 0.9030615
## 52: 0.004284669 -0.4169704 1.2196713 0.9030615
## 53: 0.004284669 -0.4169704 1.2196713 0.9030615
## 54: 0.004284669 -0.4169704 1.2196713 0.9030615
## 55: 0.004284669 -0.4169704 1.2196713 0.9030615
## 56: 0.004284669 -0.4169704 1.2196713 0.9030615
## 57: 0.004284669 -0.4169704 1.2196713 0.9030615
## 58: 0.004284669 -0.4169704 1.2196713 0.9030615
## 59: 0.005111506 -0.7566956 1.0826127 0.7640431
## 60: 0.005111506 -0.7566956 1.0826127 0.7640431
## 61: 0.005111506 -0.7566956 1.0826127 0.7640431
## 62: 0.005111506 -0.7566956 1.0826127 0.7640431
## 63: 0.005111506 -0.7566956 1.0826127 0.7640431
## 64: 0.005111506 -0.7566956 1.0826127 0.7640431
## 65: 0.005111506 -0.7566956 1.0826127 0.7640431
## 66: 0.005111506 -0.7566956 1.0826127 0.7640431
## 67: 0.005111506 -0.7566956 1.0826127 0.7640431
## 68: 0.005111506 -0.7566956 1.0826127 0.7640431
## 69: 0.005111506 -0.7566956 1.0826127 0.7640431
## 70: 0.005111506 -0.7566956 1.0826127 0.7640431
## 71: 0.005030398 -0.6409917 1.0274941 0.1121456
## 72: 0.005288863 -0.9230106 1.0459982 0.4260979
## 73: 0.004655777 -0.6065374 1.2287410 0.6115571
## 74: 0.004655777 -0.6065374 1.2287410 0.6115571
## 75: 0.004655777 -0.6065374 1.2287410 0.6115571
## 76: 0.004655777 -0.6065374 1.2287410 0.6115571
## 77: 0.005269934 -1.1054164 0.8465835 0.5423247
## 78: 0.004283939 -0.4807691 1.2864858 0.2612100
## 79: 0.004283939 -0.4807691 1.2864858 0.2612100
##           se.bp          v         c      pchi

## [1] "NOIR_2" "ORF1"   "ORF36"  "ORF59"  "ORF8"   "ORF39"  "ORF62"  "ORF48"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33

Remove genes from clusters ?

##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    21
##  2:       2    12
##  3:       7    12
##  4:       1    11
##  5:       3     9
##  6:      10     4
##  7:       5     3
##  8:       4     2
##  9:      12     2
## 10:       8     1
## 11:       9     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters